Method, System, and Device for Designing Experimental Protocol

ABSTRACT

A method for designing an experimental protocol capable of coping with more advanced processing is provided. A system according to an aspect includes at least one experimental device, a controller, and a terminal device. The controller controls the at least one experimental device to execute an experimental protocol defining processing order of the at least one experimental device. The terminal device designs the experimental protocol in a form of an oriented graph in accordance with a GUI operation performed on a specific application by a user. A plurality of nodes are selectable in the terminal device as a vertex of the oriented graph and the plurality of nodes include a processing node corresponding to processing by each of the at least one experimental device and a conditional branch node corresponding to conditional branch processing.

TECHNICAL FIELD

The present invention relates to a method, a system, and a device fordesigning an experimental protocol.

BACKGROUND ART

Conventionally, a configuration in which a user performs an experimentaccording to an experimental protocol designed on a computer is known.For example, a system disclosed in WO 2016/208623 (PTL 1) acquires anddisplays a graph in which a chain of experiments is formed in a meshshape from a database including information about the experimentalprotocol.

CITATION LIST Patent Literature

PTL 1: WO 2016/208623

SUMMARY OF INVENTION Technical Problem

In the system disclosed in PTL 1, it is possible to grasp a relationbetween a plurality of experiments associated with each of a pluralityof experimental protocols based on a hierarchical structure of theexperimental protocol defined by an inheritance relation between acertain experimental protocol and another experimental protocol in whicha part of the experimental protocol is modified. However, in the systemdisclosed in PTL 1, a plurality of processing flows included in oneprotocol are not considered, and more advanced processing cannot besupported.

The present invention has been made to solve such a problem, and anobject of the present invention is to accurately perform automaticanalysis of the experimental protocol.

Solution to Problem

A method according to an aspect of the present invention includes:receiving, from a user, a graphical user interface (GUI) operation to aspecific application; designing an experimental protocol in a form of anoriented graph in accordance with the received GUI operation, theexperimental protocol defining processing order of at least oneexperimental device; and controlling the at least one experimentaldevice to automatically execute the experimental protocol. A pluralityof nodes are selectable as a vertex of the oriented graph and theplurality of nodes include a processing node corresponding to processingby each of the at least one experimental device and a conditional branchnode corresponding to conditional branch processing.

A system according to another aspect of the present invention includesat least one experimental device, a terminal device, and a controller.The terminal device includes an input unit and a processing unit. Theinput unit receives, from a user, a GUI operation to the specificapplication. The processing unit designs an experimental protocol in aform of an oriented graph in accordance with the received GUI operation.The experimental protocol defines processing order of the at least oneexperimental device. The controller controls the at least oneexperimental device to execute the experimental protocol. A plurality ofnodes are selectable in the terminal device as a vertex of the orientedgraph and the plurality of nodes include a processing node correspondingto processing by each of the at least one experimental device and aconditional branch node corresponding to conditional branch processing.

A device still according to another aspect of the present inventioncontrols at least one experimental device to execute an experimentalprotocol defining processing order of the at least one experimentaldevice. The device includes a display unit, an input unit, and aprocessing unit. A specific application is displayed on the displayunit. The input unit receives, from a user, a GUI operation to thespecific application. The processing unit designs the experimentalprotocol in a form of an oriented graph in accordance with the GUIoperation. A plurality of nodes are selectable as a vertex of theoriented graph and the plurality of nodes include a processing nodecorresponding to processing by each of the at least one experimentaldevice and a conditional branch node corresponding to conditional branchprocessing.

Advantageous Effects of Invention

According to the method, the system, and the device of the presentinvention, the experimental protocol can be designed in the form of theoriented graph including the conditional branch node, so that the methodfor designing the experimental protocol capable of coping with moreadvanced processing can be provided.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 is a block diagram illustrating a configuration of an automaticexperiment management system according to an embodiment.

FIG. 2 is a block diagram illustrating a hardware configuration of aterminal device in FIG. 1 .

FIG. 3 is a view illustrating a GUI configuration of an experimentalprotocol design application in FIG. 1 .

FIG. 4 is a view illustrating a state in which certain processing isselected in the automatic experiment system window of FIG. 3 .

FIG. 5 is a view illustrating a state in which a processing nodecorresponding to processing selected in FIG. 4 is added to a protocoldesign window.

FIG. 6 is a view illustrating a state in which a sample containercorresponding to a container node in FIG. 5 is designated.

FIG. 7 is a view illustrating a state in which the designation of thesample container corresponding to the container node in FIG. 6 iscompleted.

FIG. 8 is a view illustrating a state in which a feature amountextraction node is added to the protocol design window in FIG. 7 .

FIG. 9 is a view illustrating a state in which output data correspondingto the data node in FIG. 8 is selected as data for which characteristicamount extraction processing corresponding to the characteristic amountextraction node is performed.

FIG. 10 is a view illustrating a state in which a conditional branchnode is added to the protocol design window in FIG. 9 .

FIG. 11 is a view illustrating a state in which conditional branchprocessing of the conditional branch node in FIG. 10 is established.

FIG. 12 is a view illustrating an oriented graph that is a designexample of another experimental protocol.

FIG. 13 is a view illustrating an oriented graph that is a designexample of another experimental protocol.

FIG. 14 is a view illustrating an example of information that isdisplayed when a predetermined GUI operation of a user is performed on anode included in the oriented graph in FIG. 13 .

FIG. 15 is a block diagram illustrating a hardware configuration of aserver device in FIG. 1 .

FIG. 16 is a flowchart illustrating a flow of an automatic experimentbased on an experiment protocol performed in the automatic experimentmanagement system of FIG. 1 .

FIG. 17 is a block diagram illustrating a configuration of an automaticexperiment management system according to a first modification of theembodiment.

FIG. 18 is a block diagram illustrating a hardware configuration of aserver device in FIG. 17 .

FIG. 19 is a block diagram illustrating a configuration of aninformation processing device according to a second modification of theembodiment.

FIG. 20 is a block diagram illustrating a hardware configuration of acontroller in FIG. 19 .

DESCRIPTION OF EMBODIMENT

Hereinafter, an embodiment will be described in detail with reference tothe drawings. In the drawings, the same or corresponding portions aredenoted by the same reference numeral, and the description will not berepeated in principle.

FIG. 1 is a block diagram illustrating a configuration of an automaticexperiment management system 1000 according to an embodiment. Asillustrated in FIG. 1 , automatic experiment management system 1000includes an automatic experiment system 1, a server device 200, adatabase 300, and a terminal device 400. Database 300 is connected toserver device 200. For example, information about automatic experimentsystem 1, information about a sample, an experiment protocol, and outputdata (experiment result) by execution of the experiment protocol areregistered in database 300. Terminal device 400 includes an input andoutput unit 430. Input and output unit 430 includes a display 431, akeyboard 432, and a touch pad 433. For example, terminal device 400 is anotebook computer, a personal computer, a smartphone, and a tablet.Automatic experiment system 1, server device 200, and terminal device400 are connected to each other through a network NW. For example,network NW includes the Internet, a wide area network (WAN), or a localarea network (LAN). The number of terminal devices connected to thenetwork NW may greater than or equal to two, and the number of automaticexperiment systems may be greater than or equal to.

Server device 200 provides an experimental protocol design application500 (specific application) as a web application to terminal device 400.Experimental protocol design application 500 is displayed on display 431through a Web browser 600 in terminal device 400. Keyboard 432 and touchpad 433 receive a GUI operation on experimental protocol designapplication 500 by a user. That is, the user of terminal device 400selects the automatic experiment system in experimental protocol designapplication 500 by the GUI operation through keyboard 432 and touch pad433, and designs the experimental protocol executed by the automaticexperiment system. The experimental protocol defines processing order ofat least one experimental device included in the automatic experimentsystem selected by the user. Terminal device 400 transmits theexperimental protocol designed by the user to server device 200. Serverdevice 200 transmits the experimental protocol to the automaticexperiment system designated by the user of terminal device 400. Serverdevice 200 can collectively manage a plurality of terminal devices and aplurality of automatic experiment systems when being interposed betweenthe terminal device that designs the experimental protocol and theautomatic experiment system that executes the experimental protocol.

Automatic experiment system 1 includes a controller 110 and a pluralityof experimental devices 120. Controller 110 controls the plurality ofexperimental devices 120 to automatically execute the experimentalprotocol from server device 200. The plurality of experimental devices120 include a robot arm 121, an incubator 122, a liquid handler 123, amicroplate reader 124, a centrifuge 125, and a liquid chromatograph massspectrometer (LCMS) 126. The number of experimental devices included inthe automatic experiment system may be one.

Robot arm 121 moves a plate Plt1 or Plt2, which is a containercontaining a sample, to the experimental device corresponding to each ofa plurality of pieces of processing according to the order of theplurality of pieces of processing defined in the experimental protocol.For example, each of plates Plt1, Plt2 contains agar containing acultured Escherichia coli. Incubator 122 cultures a cell whileperforming temperature control. Liquid handler 123 automaticallydistributes (dispenses) a certain amount of sample into each of aplurality of microplates (wells). Microplate reader 124 performsmeasurements (for example, absorbance measurement and fluorescenceintensity measurement) of an optical property of the sample in themicroplate. Centrifuge 125 separates components of the sample bycentrifugal force. LCMS 126 performs mass spectrometry separatingcomponents of the sample separated by liquid chromatograph for eachmass-to-charge ratio (m/z).

FIG. 2 is a block diagram illustrating a hardware configuration ofterminal device 400 in FIG. 1 . As illustrated in FIG. 2 , terminaldevice 400 includes a processor 421, a memory 422 and a hard disk 423 asa storage, a communication interface 424, and input and output unit 430.These are communicably connected to each other through a bus 440.

Hard disk 423 is a non-volatile storage device. For example, hard disk423 stores a program 41 of an operating system (OS) and a Web browserprogram 42. In addition to the data in FIG. 2 , for example, settingsand outputs of various applications are stored in hard disk 423. Memory422 is typically a volatile storage device such as a dynamic randomaccess memory (DRAM).

Processor 421 includes a central processing unit (CPU). Processor 421reads a program stored in hard disk 423 into memory 422 and executes theprogram. Processor 421 is connected to network NW through communicationinterface 424.

FIG. 3 is a view illustrating a GUI configuration of experimentalprotocol design application 500 in FIG. 1 . As illustrated in FIG. 3 ,experimental protocol design application 500 includes a queue listwindow 510, a protocol list window 520, a protocol design window 530, anautomated experiment system window 540, a sample container window 550, atool window 560, and a selection cursor Cr.

Queue list window 510 displays a queue in which a plurality of protocolsare ordered. In FIG. 3 , queues q1, q2 are displayed in queue listwindow 510. The experimental protocol is displayed in protocol listwindow 520. In FIG. 3 , an experimental protocol p1 is displayed andselected in protocol list window 520.

In protocol design window 530, the experimental protocol is designed ina form of an oriented graph. In the oriented graph, a connectionrelationship between a plurality of nodes is defined as an edge. Theoriented graph is stored as graph structure data according to apredetermined structured data format. For example, eXtensible MarkupLanguage (XML) and JavaScript (registered trademark) Object Notation(Json) can be cited as the structured data format. The plurality ofnodes selectable as vertices of the oriented graph are formed as GUIsand include container nodes, processing nodes, and data nodes. Thecontainer node is a node corresponding to a container containing thesample. The processing node is a node corresponding to processing byeach of the device included in the automatic experiment system. The datanode is a node corresponding to the output data of the processing of theexperimental device.

The protocol design window 530 is divided into a container region 531, aprocessing region 532, and a data region 533. In an initial state inwhich design of a certain experimental protocol is started, a start nodeMs representing a start of the experimental protocol, an end node Merepresenting an end of the experimental protocol, and an edge E10 fromthe start node Ms to the end node Me are displayed in processing region532.

Processing executable by each of at least one experimental deviceincluded in the automatic experiment system selected by the user isdisplayed in automatic experiment system window 540. In FIG. 3 ,automatic experiment system 1 is selected. “Transport of container” isdisplayed as the processing executable by robot arm 121. “Cell culture”is displayed as the processing executable by incubator 122. “Dispensingof liquid” is displayed as the processing executable by liquid handler123. “Absorbance measurement” and “fluorescence intensity measurement”are displayed as the processing executable by microplate reader 124.“Centrifugation” is displayed as the processing executable by centrifuge125. “Mass spectrometry” is displayed as the processing executable byLCMS 126.

The container containing the sample is displayed in sample containerwindow 550. In FIG. 3 , plates Plt1, Plt2 are displayed as the containerstoring the Escherichia coli that is an example of the sample.

Specific processing performed by the controller of the automaticexperiment system is displayed on tool window 560. In FIG. 3 , “featureamount extraction”, “conditional branching”, “iteration”, and “timer”are displayed. The “feature amount extraction” corresponds to processingfor extracting a feature amount designated by the user from the datacorresponding to the data node selected by the user. The “conditionalbranching” corresponds to processing for performing branching processingbased on whether a condition designated by the user is successful. The“iteration” corresponds to processing for iterating specified processinga number of times designated by the user. The “timer” corresponds toprocessing for waiting for the progressing of the experimental protocolfor a time designated by the user.

FIG. 4 is a view illustrating a state in which certain processing isselected in automatic experiment system window 540 of FIG. 3 . Asillustrated in FIG. 4 , the “absorbance measurement” is selected by theuser in automated experiment system window 540 and dragged between startnode Ms and end node Me.

FIG. 5 is a diagram illustrating a state in which the processing nodecorresponding to the processing selected in FIG. 4 is added to protocoldesign window 530. As illustrated in FIG. 5 , a processing node M1corresponding to the “absorbance measurement” is added and selectedbetween start node Ms and end node Me. Due to the addition of processingnode M1, a container node C1 and a data node D1 are automatically addedto container region 531 and data region 533, respectively. Aninformation window 570 including information about the selected node isdisplayed due to the selection of processing node M1. In FIG. 5 , ameasurement wavelength and a measurement target well are displayed asparameters of the absorbance measurement corresponding to processingnode M1.

Start node Ms and processing node M1 are connected by an edge E1 fromstart node Ms to processing node M1. Processing node M1 and end node Meare connected by an edge E2 from processing node M1 to end node Me.Container node C1 and processing node M1 are connected by an edge E3(first edge) from container node C1 to processing node M1. Processingnode M1 and data node D1 are connected by an edge E4 (second edge) fromprocessing node M1 to data node D1. Edge E3 indicates that the containercorresponding to container node C1 is input to the processingcorresponding to processing node M1. Edge E4 indicates that the outputdata of the processing corresponding to processing node M1 correspondsto data node D1. Due to the addition of the processing node, thecontainer node and the data node that are connected to the processingnode are automatically added, whereby the design of the experimentalprotocol can be made efficient. In FIG. 5 , because the sample containercorresponding to container node C1 is not designated, container node C1and edge E3 are indicated by dotted lines.

FIG. 6 is a view illustrating a state in which the sample containercorresponding to container node C1 in FIG. 5 is designated. Asillustrated in FIG. 6 , “plate Plt1” is selected in sample containerwindow 550 and dragged into vessel node C1 by the user. Due to “platePlt1” is selected in sample container window 550, a title of informationwindow 570 changes to “container information”.

FIG. 7 is a view illustrating a state in which the designation of thesample container corresponding to container node C1 in FIG. 6 iscompleted. As illustrated in FIG. 7 , container node C1 is selected, andcontainer node C1 and edge E3 are indicated in solid lines. The sampleand a container name contained in the container corresponding tocontainer node C1 are illustrated in information window 570.

FIG. 8 is a view illustrating a state in which a feature amountextraction node T1 is added to protocol design window 530 in FIG. 7 .The “feature quantity extraction” is selected in tool window 560 anddragged into protocol design window 530. As a result, feature amountextraction node T1 is added to protocol design window 530. The title ofinformation window 570 changes to “tool information” due to theselection of feature amount extraction node T1.

FIG. 9 is a view illustrating a state in which output data correspondingto data node D1 in FIG. 8 is selected as the data for whichcharacteristic amount extraction processing corresponding tocharacteristic amount extraction node T1 is performed. As illustrated inFIG. 9 , an edge E5 from data node D1 to feature amount extraction nodeT1 is added by a drag operation of the user from data node D1 to featureamount extraction node T1. Edge E5 indicates that a certain featureamount is extracted from the output data corresponding to data node D1by the feature amount extraction processing corresponding to featureamount extraction node T1. The user can designate the feature amountextracted from the output data corresponding to data node D1 in theinformation window corresponding to feature amount extraction node T1.The feature amount may be selected from a predetermined feature amounttemplate.

FIG. 10 is a view illustrating a state in which a conditional branchnode T2 is added to protocol design window 530 in FIG. 9 . Asillustrated in FIG. 10 , the “conditional branching” is selected in toolwindow 560 and dragged into protocol design window 530. As a result,conditional branch node T2 is added to protocol design window 530. Theuser may specify a condition for condition branch node T2 in informationwindow 570. For example, the condition can be input as an equality or aninequality. An edge E6 indicating that the condition of conditionalbranch node T2 is satisfied and an edge E7 indicating that the conditionis not satisfied extend from conditional branch node T2. Each of edgesE6, E7 is indicated by a dotted line because a connection destination isundetermined.

FIG. 11 is a view illustrating a state in which the conditional branchprocessing of conditional branch node T2 in FIG. 10 is established. Inan oriented graph DG1 of FIG. 11 , the position of end node Me is movedfrom the position of end node Me in FIG. 10 , and edge E2 is deleted. Anedge E8 from feature amount extraction node T1 to conditional branchnode T2 is added by the drag operation of the user from feature amountextraction node T1 to conditional branch node T2. Edge E8 indicates thata condition related to the feature amount extracted by the processingcorresponding to feature amount extraction node T1 is designated as thecondition of conditional branch node T2. A distal end of edge E6 isconnected to end node Me by the drag operation of the user on the distalend of edge E6. The distal end of edge E7 is connected to processingnode M1 by the drag operation of the user on the distal end of edge E7.The feature amount of the output data corresponding to data node D1 canbe directly used as the condition of conditional branch node T2 throughfeature amount extraction node T1, so that the design of the conditionalbranch processing based on the output data can be made efficient.

Oriented graph DG1 includes a loop structure that circulates throughprocessing node M1, data node D1, feature amount extraction node T1, andconditional branch node T2 in this order. When the condition ofcondition branch node T2 is satisfied, experimental protocol p1 ends.When the condition of condition branch node T2 is not satisfied, theprocessing of each of processing node M1 and feature amount extractionnode T1 is performed in this order, and then the conditional branchprocessing of conditional branch node T2 is performed again. While thecondition of the condition branch node T2 is not satisfied, theprocessing of each of processing node M1 and feature amount extractionnode T1 is repeated. That is, the condition of conditional branch nodeT2 is an end condition of the iterative processing including theprocessing of each of processing node M1 and feature amount extractionnode T1. The condition of the conditional branch node can also be acontinuation condition of the iterative processing. In this case, theiterative processing is continued while the condition of the conditionalbranch node is satisfied.

The conditional branch processing node is included in the plurality ofnodes selectable as a vertex of the oriented graph, so that thestructure of the conditional branch processing and the structure of theiterative processing of the experimental protocol can be accuratelyreflected in the oriented graph. As a result, the method for designingthe experimental protocol capable of coping with more advancedprocessing can be provided. In addition, the experimental protocol isdesigned in the form of the oriented graph, so that the automaticanalysis of the experimental protocol, such as tracking of the processof change of the sample in the experimental protocol, can be accuratelyperformed. For example, a lineage of cells formed by repeating seedingand subculture can be cited as the process of changing the sample in theexperimental protocol. The automatic analysis of the experimentalprotocol also includes machine learning (for example, principalcomponent analysis or deep learning) on the oriented graph.

FIG. 12 is a view illustrating an oriented graph DG2 that is a designexample of another experimental protocol p2. As illustrated in FIG. 12 ,“protocol p2” is selected in protocol list window 520. Oriented graphDG2 includes a start node Ms2, an end node Me2, a processing node M21corresponding to the absorbance measurement, a timer node T22, iterationnodes T23A, T23B, a container node C21, and a data node D21. Start nodeMs2 and iteration node T23A are connected by an edge E21 from start nodeMs2 to iteration node T23A. Iteration node T23A and processing node M21are connected by an edge E22 from iteration node T23A to processing nodeM21. Container node C21 and processing node M21 are connected by an edgeE23 from container node C21 to processing node M21. Processing node M21and data node D21 are connected by an edge E24 from processing node M21to data node D21.

Processing node M21 and timer node T22 are connected by an edge E25 fromprocessing node M21 to timer node T22. Timer node T22 and iteration nodeT23B are connected by an edge E26 from timer node T22 to iteration nodeT23B. Iteration node T23B and end node Me2 are connected by an edge E27from iteration node T23B to end node Me2. Iteration nodes T23B, T23A areconnected by an edge E28 from iteration node T23B to iteration nodeT23A. Oriented graph DG2 includes a loop structure circulating in theorder of a repetition node T23A, a processing node M21, a timer nodeT22, and an iteration node T23B. An upper limit value of the number ofiterations of the iterative processing by iteration nodes T23A, T23B isdesignated in information window 570. The end condition of the iterativeprocessing is a condition that the number of iterations is greater thanor equal to the upper limit value. The continuation condition of theiterative processing is a condition that the number of iterations issmaller than the upper limit value. The iterative node can improveefficiency in the design of the iterative processing in the experimentalprotocol.

FIG. 13 is a view illustrating an oriented graph DG3 that is a designexample of another experimental protocol p3. As illustrated in FIG. 13 ,“protocol p3” is selected in protocol list window 520. Oriented graphDG3 includes a start node Ms3, an end node Me3, processing nodes M31,M32, M33, M34, M35, M36, container nodes C31, C32, and data nodes D31,D32. Processing nodes M31 to M36 correspond to “culturing cell”,“dispensing liquid”, “absorbance measurement”, “centrifugation”,“dispensing liquid”, and “mass spectrometry”, respectively, illustratedin automated experiment system window 540.

Start node Ms3 and processing node M31 are connected by an edge E31 fromstart node Ms3 to processing node M31. Processing nodes M31, M32 areconnected by an edge E32 going from processing node M31 to processingnode M32. Processing nodes M32, M33 are connected by an edge E33 goingfrom processing node M32 to processing node M33. Processing nodes M33,M34 are connected by an edge E34 going from processing node M33 toprocessing node M34. Processing nodes M34, M35 are connected by an edgeE35 going from processing node M34 to processing node M35. Processingnodes M35, M36 are connected by an edge E36 going from processing nodeM35 to processing node M36. Processing node M36 and end node Me3 areconnected by an edge E37 from processing node M36 to end node Me.

Container node C31 and processing node M31 are connected by an edge E41from container node C31 to processing node M31. Container node C31 andprocessing node M32 are connected by an edge E42 from container node C31to processing node M32.

Container node C32 and processing node M32 are connected by an edge E43from container node C32 to processing node M32. Container node C32 andprocessing node M33 are connected by an edge E44 from container node C32to processing node M33. Container node C32 and processing node M34 areconnected by an edge E45 from container node C32 to processing node M34.Container node C32 and processing node M35 are connected by an edge E46from container node C32 to processing node M35. Container node C32 andprocessing node M36 are connected by an edge E47 from container node C32to processing node M36.

Processing node M33 and data node D31 are connected by an edge E51 fromprocessing node M33 to data node D31. Processing node M36 and data nodeD32 are connected by an edge E52 from processing node M36 to data nodeD32.

FIG. 14 is a view illustrating an example of information that isdisplayed when a predetermined GUI operation (for example, double click)of the user is performed on the node included in oriented graph DG3 inFIG. 13 . The example of the information that is displayed when the datanode D32 (selection node) in FIG. 13 is double-clicked is illustrated inFIG. 14 . FIGS. 14(a) and 14(b) illustrate a liquid chromatogram and amass spectrum produced from the output data of the mass spectrometrycorresponding to processing node M36. For example, the description ofthe processing corresponding to the processing node is displayed whenthe processing node is double-clicked. For example, the detaileddescription of the sample included in the container is displayed whenthe container node is double-clicked. When the information about thenode is displayed by a predetermined GUI operation on the node of theoriented graph, the information about the components of the experimentalprotocol designed in the form of the oriented graph can be efficientlyreferred to.

FIG. 15 is a block diagram illustrating a hardware configuration ofserver device 200 in FIG. 1 . As illustrated in FIG. 15 , server device200 includes a processor 201, a memory 202 and a hard disk 203 as astorage, a communication interface 204 as a communication unit, and aninput and output unit 205. These are communicably connected to eachother through a bus 210.

Hard disk 203 is a non-volatile storage device. For example, hard disk203 stores a program 51 of an operating system (OS) and an automaticexperiment management program 52. In addition to the data in FIG. 15 ,for example, settings and outputs of various applications are stored inhard disk 203. Memory 202 is typically a volatile storage device such asa dynamic random access memory (DRAM).

Processor 201 includes a central processing unit (CPU). Processor 201reads a program stored in hard disk 203 into memory 202 and executes theprogram to implement various functions of server device 200. Forexample, processor 201 executing automatic experiment management program52 provides experimental protocol design application 500 to terminaldevice 400. Processor 201 is connected to network NW throughcommunication interface 204.

FIG. 16 is a flowchart illustrating a flow of an automatic experimentbased on the experiment protocol performed in automatic experimentmanagement system 1000 of FIG. 1 . As illustrated in FIG. 16 , in S11,terminal device 400 designs the experimental protocol in the form of theoriented graph, and transmits the experimental protocol to server device200. In S12, server device 200 transmits the experimental protocol tothe automatic experiment system selected by the user of terminal device400. In S13, the controller of the automatic experiment systemautomatically executes the experiment protocol received from serverdevice 200. In step S14, the controller transmits the output data of theprocessing included in the experimental protocol to server device 200.

In the embodiment, the case where the experimental protocol designed inthe terminal device is transmitted to the automatic experiment systemthrough the server device has been described. The experimental protocolmay be directly transmitted from the terminal device to the automaticexperiment system.

FIG. 17 is a block diagram illustrating a configuration of an automaticexperiment management system 1100 according to a first modification ofthe embodiment. The configuration of automatic experiment managementsystem 1100 is a configuration in which server device 200 and database300 are excluded from automatic experiment management system 1000 inFIG. 1 and terminal device 400 is replaced with a terminal device 400A.The other configurations are the same, and the description thereof willnot be repeated. An experimental protocol design application 500A isdisplayed on display 431 of terminal device 400A.

FIG. 18 is a block diagram illustrating a hardware configuration ofterminal device 400A in FIG. 17 . The configuration of terminal device400A is a configuration in which an automatic experiment managementprogram 52A is added to hard disk 423 in FIG. 2 . Because otherconfigurations are the same, the description thereof will not berepeated. The automatic execution of the experimental protocol byexperimental protocol design application 500A and the automaticexperiment system is implemented when automatic experiment managementprogram 52A is executed by processor 421.

The experimental protocol may be designed in the controller of theautomated experiment system. FIG. 19 is a block diagram illustrating aconfiguration of an automatic experiment system 1B according to a secondmodification of the embodiment. The configuration of automaticexperiment system 1B is a configuration in which controller 110 isreplaced with a controller 110B in automatic experiment system 1 of FIG.1 . Because other configurations are the same, the description thereofwill not be repeated.

As illustrated in FIG. 19 , controller 110B includes an input and outputunit 130 and a computer 140 (processing unit). Input and output unit 130includes a display 131 (display unit), a keyboard 132 (input unit), anda mouse 133 (input unit). Display 131, mouse 133, and keyboard 132 areconnected to computer 140. A GUI of experimental protocol designapplication 500B is displayed on display 131. Keyboard 132 and mouse 133receive the GUI operation on experimental protocol design application500B by the user. That is, the user performs the desired GUI operationon experimental protocol design application 500B by the operation ofoperating keyboard 132 or mouse 133 while the display of display 131 isreferred to.

FIG. 20 is a block diagram illustrating a hardware configuration ofcontroller 110B in FIG. 19 . As illustrated in FIG. 20 , computer 140includes a processor 141, a memory 142 and a hard disk 143 as a storage,and a communication interface 144. These are communicably connected toeach other through a bus 145.

Hard disk 143 is a non-volatile storage device. For example, a program61 of an operating system (OS) and an automatic experiment managementprogram 52B are stored in hard disk 143. In addition to the data in FIG.20 , for example, settings and outputs of various applications arestored in hard disk 143. Memory 142 is typically a volatile storagedevice such as a dynamic random access memory (DRAM).

Processor 141 includes a central processing unit (CPU). Processor 141reads a program stored in hard disk 143 into memory 142 and executes theprogram. The automatic execution of the experimental protocol byexperimental protocol design application 500B and the plurality ofexperimental devices 120 is implemented when automatic experimentmanagement program 52B is executed by processor 141. Processor 141 isconnected to network NW through communication interface 144.

As described above, the method for designing the experimental protocolthat can cope with more advanced processing can be provided according tothe methods and systems of the embodiment and the first modification andthe device of the second modification of the embodiment.

[Aspects]

It is understood by those skilled in the art that the embodimentdescribed above are specific examples of the following aspects.

(Item 1)

A method according to an aspect of the present invention includes:receiving, from a user, a GUI operation to a specific application;designing an experimental protocol in a form of an oriented graph inaccordance with the received GUI operation, the experimental protocoldefining processing order of at least one experimental device; andcontrolling the at least one experimental device to automaticallyexecute the experimental protocol. A plurality of nodes are selectableas a vertex of the oriented graph and the plurality of nodes include aprocessing node corresponding to processing by each of the at least oneexperimental device and a conditional branch node corresponding toconditional branch processing.

According to the method described in item 1, the experimental protocolcan be designed in the form of the oriented graph including theconditional branch node, so that the method for designing theexperimental protocol capable of coping with more advanced processingcan be provided.

(Item 2)

The method described in item 1, wherein the plurality of nodes furtherinclude a container node, a data node, and a feature amount extractionnode. The container node corresponds to a container containing a sampleprocessed by the at least one experimental device. The data nodecorresponds to output data of processing on the sample by each of the atleast one experimental device. The feature amount extraction nodecorresponds to processing for extracting a feature amount from theoutput data. A condition of the conditional branch node includes acondition related to the feature amount.

According to the method described in item 2, since the feature amount ofthe output data corresponding to the data node can be directly used forthe condition of the conditional branch node through the feature amountextraction node, so that the design of the conditional branch processingbased on the output data can be made efficient.

(Item 3)

In the method described in item 2, designing the experimental protocolin the form of the oriented graph includes automatically adding thecontainer node and the data node due to the addition of the processingnode. At this point, the container node and the processing node areconnected by a first edge from the container node to the processingnode. The processing node and the data node are connected by a secondedge from the processing node to the data node.

According to the method described in item 3, the container node and thedata node connected to the processing node are automatically added dueto the addition of the processing node, whereby the design of theexperimental protocol can be made efficient.

(Item 4)

In the method described in any one of items 1 to 3, information about aselection node is displayed in response to a predetermined GUI operationon the selection node included in the plurality of nodes.

According to the method described in item 4, when the information aboutthe selection node is displayed by the predetermined GUI operation onthe selection node, the information about a component of theexperimental protocol designed in the form of the oriented graph can beefficiently referred to.

(Item 5)

In the method according to any one of items 1 to 4, the plurality ofnodes further include an iterative node corresponding to iterativeprocessing.

According to the method described in item 5, the iterative node canimprove efficiency in the design of the iterative processing in theexperimental protocol.

(Item 6)

A system according to another aspect includes at least one experimentaldevice, a terminal device, and a controller. The terminal deviceincludes an input unit and a processing unit. The input unit receives,from a user, a GUI operation to a specific application. The processingunit designs an experimental protocol in a form of an oriented graph inaccordance with the received GUI operation. The experimental protocoldefines processing order of the at least one experimental device. Thecontroller controls the at least one experimental device to execute theexperimental protocol. A plurality of nodes are selectable in theterminal device as a vertex of the oriented graph and the plurality ofnodes include a processing node corresponding to processing by each ofthe at least one experimental device and a conditional branch nodecorresponding to conditional branch processing.

According to the system described in item 6, the experimental protocolcan be designed in the form of the oriented graph including conditionalbranch nodes, so that the method for designing the experimental protocolcapable of coping with more advanced processing can be provided.

(Item 7)

The system described in item 6 further includes a server device thatprovides the specific application to the terminal device. The serverdevice transmits the experimental protocol designed in the terminaldevice to the controller.

According to the system described in item 7, the server device isinterposed between the terminal device that designs the experimentalprotocol and the controller that controls and executes at least oneexperimental device of the experimental protocol, whereby the serverdevice can collectively manage the plurality of terminal devices and theplurality of controllers.

(Item 8)

A device according to still another aspect controls at least oneexperimental device to execute an experimental protocol definingprocessing order of the at least one experimental device. The deviceincludes a display unit, an input unit, and a processing unit. Aspecific application is displayed on the display unit. The input unitreceives, from a user, a GUI operation to the specific application. Theprocessing unit designs the experimental protocol in a form of anoriented graph in accordance with the GUI operation. A plurality ofnodes are selectable as a vertex of the oriented graph and the pluralityof nodes include a processing node corresponding to processing by eachof the at least one experimental device and a conditional branch nodecorresponding to conditional branch processing.

According to the device described in item 8, the experimental protocolcan be designed in the form of the oriented graph including theconditional branch node, so that the method for designing theexperimental protocol capable of coping with more advanced processingcan be provided.

For the above-described embodiment and modification, it is planned fromthe beginning of the application to appropriately combine theconfigurations described in the embodiments within a range in which noinconvenience or contradiction occurs including combinations notmentioned in the specification.

It should be considered that the disclosed embodiment is an example inall respects and not restrictive. The scope of the present invention isdefined by not the description above, but the claims, and it is intendedthat all modifications within the meaning and scope of the claims andtheir equivalents are included in the present invention.

REFERENCE SIGNS LIST

1, 1B: automatic experiment system, 110, 110B: controller, 120:experimental device, 121: robot arm, 122: incubator, 123: liquidhandler, 124: microplate reader, 125: centrifuge, 130, 205, 430: inputand output unit, 131, 431: display, 132, 432: keyboard, 133: mouse, 140:computer, 141, 201, 421: processor, 142, 202, 422: memory, 143, 203,423: hard disk, 144, 204, 424: communication interface, 145, 210, 440:bus, 200: server device, 300: database, 400, 400A: terminal device, 433:touch pad, 500, 500A, 500B: experimental protocol design application,510: queue list window, 520: protocol list window, 530: protocol designwindow, 531: container region, 532: processing region, 533: data region,540: automatic experiment system window, 550: sample container window,560: tool window, 570: information window, 600: Web browser, 1000, 1100:automatic experiment management system, C1, C21, C31, C32: containernode, Cr: selection cursor, D1, D21, D31, D32: data node, DG1 to DG3:oriented graph, T2: conditional branch node, M1, M21, M31 to M36:processing node, T1: feature amount extraction node, T23A, T23B:iterative node, Me, Me2, Me3: end node, Ms, Ms2, Ms3: start node, NW:network, Plt1, Plt2: plate, T22: timer node, p1 to p3: experimentalprotocol

1. A method comprising: receiving, from a user, a graphical userinterface (GUI) operation to a specific application; designing anexperimental protocol in a form of an oriented graph in accordance withthe received GUI operation, the experimental protocol definingprocessing order of at least one experimental device; and controllingthe at least one experimental device to automatically execute theexperimental protocol, wherein a plurality of nodes are selectable as avertex of the oriented graph and the plurality of nodes include aprocessing node corresponding to processing by each of the at least oneexperimental device and a conditional branch node corresponding toconditional branch processing, and designing the experimental protocolin the form of the oriented graph includes changing a connectionrelationship between the processing node and the conditional branch nodeaccording to the received GUI operation.
 2. The method according toclaim 1, wherein the plurality of nodes further includes: a containernode corresponding to a container containing a sample processed by theat least one experimental device; a data node corresponding to outputdata of processing on the sample by each of the at least oneexperimental device; and a feature amount extraction node correspondingto processing for extracting a feature amount from the output data, anda condition of the conditional branch node includes a condition relatedto the feature amount.
 3. The method according to claim 2, whereindesigning the experimental protocol in the form of the oriented graphincludes automatically adding the container node and the data node dueto the addition of the processing node, the container node and theprocessing node are connected by a first edge from the container node tothe processing node, and the processing node and the data node areconnected by a second edge from the processing node to the data node. 4.The method according to claim 1, wherein information about a selectionnode is displayed in response to a predetermined GUI operation on theselection node included in the plurality of nodes.
 5. The methodaccording to claim 1, wherein the plurality of nodes further includes aniterative node corresponding to iterative processing.
 6. A systemcomprising: at least one experimental device; a terminal device thatincludes an input unit that receives, from a user, a GUI operation to aspecific application and a processing unit that designs an experimentalprotocol in a form of an oriented graph in accordance with the receivedGUI operation, the experimental protocol defining processing order ofthe at least one experimental device; and a controller that controls theat least one experimental device to execute the experimental protocol,wherein a plurality of nodes are selectable in the terminal device as avertex of the oriented graph and the plurality of nodes include aprocessing node corresponding to processing by each of the at least oneexperimental device and a conditional branch node corresponding toconditional branch processing.
 7. The system according to claim 6,further comprising a server device that provides the specificapplication to the terminal device, wherein the server device transmitsthe experimental protocol designed in the terminal device to thecontroller.
 8. (canceled)
 9. A method comprising: receiving, by a user,a graphical user interface (GUI) operation to a specific application;designing an experimental protocol in a form of an oriented graph inaccordance with the received GUI operation, the experimental protocoldefining processing order of at least one experimental device; andcontrolling the at least one experimental device to automaticallyexecute the experimental protocol, wherein the at least one experimentaldevice includes an analysis device, a plurality of nodes are selectableas a vertex of the oriented graph and the plurality of nodes include adata node corresponding to output data of processing by the analysisdevice, and the method further comprises displaying, based on selection,by a user, of the data node, at least one of a chromatogram and aspectrum produced from the output data corresponding to the data node.